MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b3942 b1732 b3708 b3008 b3752 b0871 b2925 b2097 b2407 b3236 b2883 b2690 b2797 b3117 b1814 b4471 b2210 b3945 b4381 b2868 b4064 b4464 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b3927 b1380 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.588899 (mmol/gDw/h)
  Minimum Production Rate : 0.090118 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.422792
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.889679
  EX_pi_e : 0.838411
  EX_so4_e : 0.148297
  EX_k_e : 0.114949
  EX_fe2_e : 0.009458
  EX_mg2_e : 0.005109
  EX_ca2_e : 0.003065
  EX_cl_e : 0.003065
  EX_cu2_e : 0.000418
  EX_mn2_e : 0.000407
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.672309
  EX_co2_e : 27.128008
  EX_h_e : 8.333816
  EX_pyr_e : 2.573394
  Auxiliary production reaction : 0.090118
  EX_ade_e : 0.015805
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000131

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 21-Sep-2023
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